/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.analysis;
import static org.junit.Assert.*;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import org.junit.Before;
import org.junit.Test;
/**
* Test the alignment -> Mapping routines
* @author jimp
*
*/
public class TestAlignSeq
{
SequenceI s1,s2,s3;
/**
* @throws java.lang.Exception
*/
@Before
public void setUp() throws Exception
{
s1 = new Sequence("Seq1","ASDFAQQQRRRSSS");
s1.setStart(3);
s2 = new Sequence("Seq2","ASDFA");
s2.setStart(5);
s3 = new Sequence("Seq1","SDFAQQQSSS");
}
@Test
/**
* simple test that mapping from alignment corresponds identical positions.
*/
public void TestGetMappingForS1()
{
jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
System.out.println("s1: "+as.getAStr1());
System.out.println("s2: "+as.getAStr2());
Mapping s1tos2=as.getMappingFromS1(false);
System.out.println(s1tos2.getMap().toString());
for (int i=s2.getStart();i